Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CHD6

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPSC derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
neural crest cells
cell type
iPSC-derived neural crest cells CHD6 wild type
passages
3-4
chip antibody
A301-221 Bethyl CHD6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each batch of ChIP experiments ~12 million cells were crosslinked in 2% PFA for 45 min at 4°C. From this point onward, cells were processed via the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer's instructions, but using the NEXSON protocol for the isolation of nuclei [1]. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 20-26 cycles of 30s “on” and 30s “off”, at the highest power setting), and immunoprecipitations were carried out by adding 4 μg of the appropriate antiserum (CHD6, A301-221A Bethyl; TF3B, A303-673A Bethyl) to ~30 μg of chromatin and incubating on a rotator overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research) and used in qPCR or sequencing on a HiSeq4000 platform (Illumina). For each batch of ChIP experiments ~12 million cells were crosslinked in 2% PFA for 45 min at 4°C. From this point onward, cells were processed via the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer's instructions, but using the NEXSON protocol for the isolation of nuclei [1]. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 20-26 cycles of 30s “on” and 30s “off”, at the highest power setting), and immunoprecipitations were carried out by adding 4 μg of the appropriate antiserum (CHD6, A301-221A Bethyl; TF3B, A303-673A Bethyl) to ~30 μg of chromatin and incubating on a rotator overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research) and used in qPCR or sequencing on a HiSeq4000 platform (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
82233657
Reads aligned (%)
98.1
Duplicates removed (%)
16.9
Number of peaks
2278 (qval < 1E-05)

hg19

Number of total reads
82233657
Reads aligned (%)
97.6
Duplicates removed (%)
17.8
Number of peaks
2173 (qval < 1E-05)

Base call quality data from DBCLS SRA